[phenixbb] CASP 10: Call for targets to assess the state of the art in protein structure modeling

[Torsten Schwede]

*CASP 10: Call for targets to assess the state of the art in protein 
structure modeling*

As many of you know, CASP (Critical Assessment of Structure prediction) 
has been assessing the state of the art in modeling protein structure 
from sequence since 1994, running a community experiment once every two 
years. In these experiments, information on soon to be solved structures 
is collected from the experimental community, and the sequence data are 
passed to the structure modeling community so that blind predictions of 
structure and can collected and assessed (1).  Over that period CASP has 
seen enormous progress in the quality of modeled structures (2), but 
many problems remain. CASP is only possible because of the generous 
participation of the experimental community in providing the modeling 
targets (3). We recently appealed for your help in providing novel fold 
and membrane protein targets for the ongoing CASP ROLL process. That is 
very successful, with 57 prediction teams participating and 26 targets 
already released, thanks to all of you who have contributed.

The prediction season for the next full biannual experiment, CASP 10, 
begins May 1, and so we are now asking for your help again, this time in 
reaching our goal of releasing at least varied 100 targets in a the 
three-month period. We need all sorts of targets, spanning the 
categories below:

1. (More than ever) novel folds and membrane protein targets -- even 
with the extended collection season provided by CASP ROLL, there will be 
still a shortage. There are some interesting methods developments for ab 
initio modeling, and it is important to be able to decisively evaluate 
their effectiveness.

2. A diversity of comparative modeling targets. Cases where the there is 
fairly high sequence identity (30-50%) between the target structure and 
an available template are valuable for testing the degree to which model 
accuracy can approach that of experiment, particularly in functionally 
critical regions. Cases with lower sequence identity to template, right 
down to undetectable, are valuable for testing the ability of the 
methods to detect remote homologs, to overcome challenging alignment 
difficulties, to make use of multiple templates, and to build regions of 
the structure not obviously available from a template.

3. Targets containing significant amounts of disordered structure, so as 
to test the ability of methods to identify these regions. Disorder 
identified by absence of density in crystallography is current the main 
source and very useful, but its important to have cases where the nature 
of the disorder has been established by other means, such as NMR.

4. Some targets will also be used to test methods of structure 
refinement. In these cases, the best model received for a target will be 
released to the refinement community, who will subsequently submit new 
models. This too is an area where there have been some exciting 
developments in the last year, so we are hoping for significant 
progress. Refinement targets are selected based on the nature of the 
errors in the initial models. Because of the extended process, these 
targets need to be available for longer before release of the 
experimental structure.

For those of you who have not provided targets to CASP before, the 
procedure is simple. There are three ways to submit targets: (1) Go the 
target submission web page and fill in the easy form; (2) When you 
submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, 
automatically setting up a target entry; (3) Send an email the 
prediction center with details. If you have queries, there is a very 
experienced prediction center staff to deal with them. The key thing is 
timing: We need a window of at least four weeks between receiving 
information about a target and the release of your experimental 
structure. A longer window -- up to eight weeks - is often useful, for 
example so that a target can be used to test refinement methods, but is 
not essential (note that using the PDB target submission route 
automatically selects eight weeks). We don't need your experimental 
structure in advance of its release by the PDB, provided that will 
happen by the end of August. Please consult the target submission page 
for more details: 
http://www.predictioncenter.org/casp10/targets_submission.cgi

There are already over 200 prediction teams signed for CASP 10, and so 
any targets provided will receive plenty of attention. If you have a 
suitable target now, we are ready to receive it. If new targets come up 
before July 17, we would also love to have them. (After July 17, we will 
continue with CASP ROLL for novel folds and membrane proteins). So 
please get in touch whenever a suitable opportunity arises, and help 
improve modeling methods.

Thanks,
CASP organizing committee
John Moult, IBBR, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland
Anna Tramontano, University of Rome, Italy

Get in touch: casp at predictioncenter.org
More information: http://www.predictioncenter.org/casp10/index.cgi
CASP Roll targets so far: 
http://www.predictioncenter.org/casprol/targetlist.cgi
Submit a target: 
http://www.predictioncenter.org/casp10/targets_submission.cgi

1. Critical assessment of methods of protein structure prediction 
(CASP)--round IX. <http://www.ncbi.nlm.nih.gov/pubmed/21997831>
Moult J, Fidelis K, Kryshtafovych A, Tramontano A.
Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14.

2. CASP9 results compared to those of previous CASP experiments. 
<http://www.ncbi.nlm.nih.gov/pubmed/21997643>
Kryshtafovych A, Fidelis K, Moult J.
Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011 
Oct 14

3.Target highlights in CASP9: Experimental target structures for the 
critical assessment of techniques for protein structure prediction. 
<http://www.ncbi.nlm.nih.gov/pubmed/22020785>
Kryshtafovych A et al.
Proteins 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120511/85c16308/attachment.htm>